- phenixbb - phenix-online.org

Re: [phenixbb] scaling
by Thomas C. Terwilliger 20 Jun '09

20 Jun '09

Hi, You can use autosol to do scaling of any pair of datasets, so if you just run the command below N times, once for each reference/to-be-scaled dataset pair you are interested in, it should do what you want: phenix.autosol native.data=native.sca deriv.data=deriv.sca correct_aniso=false skip_xtriage=true res_hyss=100 build=false this will stop with " HYSS failed...Probably no iso or ano differences.." because we are not giving HYSS any data. Then the file: AutoSol_run_1_/TEMP0/AutoSol_run_1_/TEMP0/mir_fbar.mtz will have the scaled native and deriv data in mtz format. For subsequent runs, the data will be in AutoSol_run_2_ ...etc I hope that helps! -Tom T >>> where ought i look for a phenx utility to scale any number of data sets >>> to >>> a reference data set? something akin to scale.inp in CNS. >> >> I don't think we have such a utility, unless there is something in >> solve (Tom?). -- But you shouldn't need this for any of the phenix >> applications. All trivial scaling of the scale.inp type is done >> on-the-fly. >> Ralf >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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scaling
by Bryan W. Lepore 19 Jun '09

19 Jun '09

where ought i look for a phenx utility to scale any number of data sets to a reference data set? something akin to scale.inp in CNS. -bryan

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Can I limit the model's B factor range during refinement
by junfeng liu 18 Jun '09

18 Jun '09

Dear all, Several models have been refined using Phenix recently. It works well . But the model's B factors in some region are very high, higher than 150 or more. Of course, the wilson B is high too, about 60-70. I remembered that the B factor can be limited in the refinement using Refmac. Can I do the similar thing in Phenix ? Thanks in advance! Best wishes, leo

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Molecular replacement
by Colin Levy 17 Jun '09

17 Jun '09

Within Phenix, is it possible to specify and lock the centre of rotation for a molecular replacement search. I have a single intrinsic anomalous scatterer within my protein which I can locate easily, therefore I would like to manually specify this point as the centre of rotation and then carry out a rotation search only about this single fixed point. Thanks for any suggestions, Colin

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Re: [phenixbb] Adding H atoms onto ligand
by Young-Jin Cho 16 Jun '09

16 Jun '09

Thanks a lot Nigel, I could generate new .cif file. Then I need to combine this ligand information while I am adding H atoms to model.pdb (protein+ligand). when I simply type "phenix.ready_set model.pdb" it will wrongly generate strange.pdb file. My question is how I can add this new geometry information (.cif file) while adding H atoms into modle.pdb file to make protein and ligand has H atoms in correct way. Thanks again in advace. YoungJin ----- Original Message ----- From: "Nigel W Moriarty" <NWMoriarty(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Tuesday, June 16, 2009 12:18:50 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Adding H atoms onto ligand YoungJin If you opened the CIF in REEL you can right-click on the P-N bond and change the order to single. You can then use the menu Action -> Build -> Add Atom to add a hydrogen to the nitrogen by clicking on the nitrogen. Nigel On 6/16/09 9:03 AM, Young-Jin Cho wrote: Thanks Nigel, I opened ANP and truncated the terminal PO3 and ran phenix.ready_set. When I opened through phenix.reel, N atom has double bond to PB, thus has only one H atom, which I thought it should be single bond thus has two H atoms like any N6 of adenine. So if you can tell me how I can handle to put correct geometry, it will be great. Cheers, YoungJin ----- Original Message ----- From: "Nigel W Moriarty" <NWMoriarty(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Tuesday, June 16, 2009 11:21:18 AM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Adding H atoms onto ligand Young-Jin You need to check that you and the PDB ligand database are talking about the same thing. You can see what the ligand ANP is by phenix.reel --chemical-components=ANP If you have the non-hydrogen atoms of your truncated ligand, phenix.ready_set will add the hydrogens and may even add the correct number of hydrogens to the terminal nitrogen. But what about its name? I would recommend find the three-letter code that corresponds to your ligand. Nigel On 6/15/09 7:01 PM, Young-Jin Cho wrote: Let me excuse to post another similar issue. I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb. As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's. I did Molprobity as in the general case to add H atoms, but it didn't make it. Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below: Processing inputs. This may take a minute or two. Sorry: Ambiguous parameter definition: remove = element H Best matches: refinement.refine.occupancies.remove_selection refinement.geometry_restraints.remove.angles refinement.geometry_restraints.remove.dihedrals refinement.geometry_restraints.remove.chiralities refinement.geometry_restraints.remove.planarities Thanks in advance, YoungJin ps. Tanks Nat! _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Adding H atoms onto ligand
by Young-Jin Cho 16 Jun '09

16 Jun '09

Let me excuse to post another similar issue. I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb. As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's. I did Molprobity as in the general case to add H atoms, but it didn't make it. Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below: Processing inputs. This may take a minute or two. Sorry: Ambiguous parameter definition: remove = element H Best matches: refinement.refine.occupancies.remove_selection refinement.geometry_restraints.remove.angles refinement.geometry_restraints.remove.dihedrals refinement.geometry_restraints.remove.chiralities refinement.geometry_restraints.remove.planarities Thanks in advance, YoungJin ps. Tanks Nat!

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specification of column labels in command line promt
by Raja Dey 15 Jun '09

15 Jun '09

Dear Friend, I was trying to analyse one of my data set. I am getting the following error. Multiple equally suitable arrays of observed xray data found. Possible choices: Cam-pk-hr_scala1.mtz:IMEAN_pk,SIGIMEAN_pk Cam-pk-hr_scala1.mtz:I_pk(+),SIGI_pk(+),I_pk(-),SIGI_pk(-),merged Please use scaling.input.xray_data.obs_labels to specify an unambiguous substring of the target label. Sorry: Multiple equally suitable arrays of observed xray data found. I have the following column labels in my .mtz file * Column Labels : H K L FreeR_flag F_pk SIGF_pk F_pk(+) SIGF_pk(+) F_pk(-) SIGF_pk(-) DANO_pk SIGDANO_pk IMEAN_pk SIGIMEAN_pk I_pk(+) SIGI_pk(+) I_pk(-) SIGI_pk(-) How I can specify column labels in a command line promt? Say, I want to use IMEAN_pk & SIGIMEAN_pk Thanks... Raja

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phenix and PAE kernels
by nick＠silvaggi.com 15 Jun '09

15 Jun '09

Dear List, Sorry if this is a naive question, but is there a known bug with phenix (or python?) on PAE kernels? I have looked on phenix-online.org, but did not find anything. This problem is independent of the phenix version (I have tried 1.4-92, 1.4-3, 1.3, and several releases of cci_apps) and occurs with almost all of the programs (most fail in the cci_apps test_apps script). The problem appears to be specific to the PAE kernels, since the same programs run fine in the non-PAE counterparts. I am running Fedora 10 with kernel versions 2.6.27.24-170.2.68/PAE and 2.6.27.21-170.2.56/PAE. Phenix programs fail under both PAE kernels, but are fine under the non-PAE kernels. Thanks in advance for any help you can provide. Best regards, Nick Silvaggi long int too large to convert Traceback (most recent call last): File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/builder.py", line 10, in <module> from elbow.chemistry.any_chemical_format_reader \ File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/any_chemical_format_reader.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/SimpleMoleculeClass.py", line 16, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/utilities/monomer_utilities.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 4, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/mmtbx/mmtbx/refinement/print_statistics.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 1, in <module> # packaging File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 518, in <module> File "/usr/swr/cci_apps/cci_apps_sources/boost_adaptbx/boost/python.py", line 68, in __init__ OverflowError: long int too large to convert

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phenix refine
by sbiswas2＠ncsu.edu 12 Jun '09

12 Jun '09

Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J " ... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42 Does anyone know how to resolve this thanks, Shya

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phasine error
by vennila Natesan 11 Jun '09

11 Jun '09

Dear members I am having solved strcutures for some five datasets of the same protein. All the cases autobuild builds ~97% of residues. I want to compare the phasing among those. Can we calculate the phasing error in the units of degrees in autosol? In all the cases, the Bayesian CC is between 45 and 56 and FOM is between 0.42 and 0.47.Is there any option in phenix to know the phasing error in degrees?

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not enough memory error in Resolve/AutobuildWizard
by Tatyana Sysoeva 10 Jun '09

10 Jun '09

Hello! I'm trying to run AutobuildWizard on distant computer cluster. Runs failed. In Autobuild log file there is a message: *TRIED resolve_giant ...NEED A BIGGER VERSION... TRIED resolve ...NEED A BIGGER VERSION... TRIED resolve_giant ...NEED A BIGGER VERSION... TRIED resolve_huge ...NEED A BIGGER VERSION... child process stderr output: command: 'AutoBuild_run_1_/TEMP0/temporary.com' Sorry, not enough memory for RESOLVE ---------------------------------- TRIED resolve_extra_huge ...but not OK ******************************************************************************** Failed to carry out AutoBuild_set_up_build: ******************************************************************************** * Some Autobuild runs were ok, some stopped with that error message. What am I doing wrong? I installed Phenix1.4-3, locally to my home folder, run it from script file in queue. As I found this Linux computer cluster has next parameters - 1 login node: -Sun SunFire v20z 1U Rackmount Box -Dual 2.4 GHz AMD Opteron Processors -8 GB of ECC RAM Could you advise something to start with to find a problem? Sincerely, Tanya

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Water/residue alternative conformations
by Roeland Boer 08 Jun '09

08 Jun '09

Dear all, I'm refining a 1.45 Ang structure in which I have several residues that have alternate conformations. These alternate conformations in some cases coincide with additional density that suggests the presence of a water molecule, appropriately positioned to make hydrogen bonds with near atoms. I have modeled partially occupied waters in these additional densities and linked their occupancies with the alternate conformation that is not clashing with the water in question. My problem is that these partially occupied waters are pushed away by the 'overlapping' alternate conformation of the amino acids. I guess there's an antibump restraint somewhere? How can I tell phenix that these alternate waters are not sterically clashing with the amino acid (since the sum occupancies of the water plus alternate conformation is 1)? The attached image shows one of those disordered residues after refinement. Water 1519 is pushed away from one alt conf (A) of Gln13, whereas the density suggests it should be making a hydrogen bond to OE1 of the altconf B of Gln13. I describe the occupancies of the situation in the attached image as below. refinement { refine { occupancies { constrained_group { selection = chain A and resseq 13 and altloc A selection = (chain A and resseq 13 and altloc B) or (resname HOH and resseq 1519 and altloc A) } } } } Thanks, Roeland Boer.

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Re: [phenixbb] autosol error 1.4-3 when trying to specify deriv.inano=noinano
by Thomas C. Terwilliger 07 Jun '09

07 Jun '09

Hi Francis, Thanks again for the files. They did help me debug the autosol wizard for this case. It turns out that on the command line you cannot say something like, native.data=nat.mtz native.labels="I SIGI" \ deriv.data=deriv.mtz deriv.labels="I+ SIGI+ I- SIGI-" deriv.inano=inano because only the first native.something= gets read, the others are ignored, and similarly only the first deriv.something= gets read. instead all this has to go in a parameters file, and then it all works fine. I have adjusted the wizard to catch this situation and to stop and tell the user that they need to use a parameters file to set more than one parameter in the native, deriv, or wavelength scopes. All the best, Tom T

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coordinates and map shifted after phenix.refine without simulated annealing
by hari jayaram 06 Jun '09

06 Jun '09

Hi i am using phenix version 1.4 release tag 70 hari@charlie:~$ phenix.refine --version ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.4 Release tag: 70 Platform: intel-linux-2.6-x86_64 linux User: hari ------------------------------------------------------------------------------- I am seeing a strange shifting of my coordinates "out of my experimental phases map" before and after refinement without simulated annelaing I am at the final stages of my refinement. When I refine without simulated annealing the resulting model is shifted relative to my experimental phases map into which I build my model The phenix command line strategy i am using are rigid_body+individual_sites+individual_adp+tls .or the same strategy with simulated_annealing=true The output map coefficients fortunately match my model in both cases . But I am wondering why there is a difference. I am using the mlhl target for refinement to 3.1 A , My R and rfree is 28/31 . Any ideas why my model shifts without simulated annealing . All pdbs have the same CRYST record . I am using coot version 0.61 for my building and map display using fft inside of coot . hari

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Re: [phenixbb] coordinates and map shifted after phenix.refine without simulated annealing
by Thomas C. Terwilliger 06 Jun '09

06 Jun '09

Hi Hari, What is your space group? I am guessing that the shift is along an axis where the origin is not fixed, for example the b axis in P21. This could happen with rigid-body refinement where a molecule can move as a whole so that the center of mass could move along that axis. Perhaps someone else can comment as to whether there is or could be an optional term in phenix.refine to maintain the center of mass at the same coordinate in such cases. All the best, Tom T >> Hi i am using phenix version 1.4 release tag 70 >> >> hari@charlie:~$ phenix.refine --version >> ------------------------------------------------------------------------------- >> PHENIX: Python-based Hierarchical ENvironment for Integrated >> Xtallography >> Version: 1.4 >> Release tag: 70 >> Platform: intel-linux-2.6-x86_64 linux >> User: hari >> ------------------------------------------------------------------------------- >> >> >> I am seeing a strange shifting of my coordinates "out of my experimental >> phases map" before and after refinement without simulated annelaing >> >> I am at the final stages of my refinement. When I refine without simulated >> annealing the resulting model is shifted relative to my experimental >> phases >> map into which I build my model >> The phenix command line strategy i am using are >> rigid_body+individual_sites+individual_adp+tls .or the same strategy with >> simulated_annealing=true >> >> The output map coefficients fortunately match my model in both cases . But >> I >> am wondering why there is a difference. >> I am using the mlhl target for refinement to 3.1 A , My R and rfree is >> 28/31 >> . >> >> Any ideas why my model shifts without simulated annealing . All pdbs have >> the same CRYST record . >> I am using coot version 0.61 for my building and map display using fft >> inside of coot . >> >> >> hari >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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autosol error 1.4-3 when trying to specify deriv.inano=noinano
by Francis E Reyes 05 Jun '09

05 Jun '09

------------------------------------------------------------ Starting AutoSol with the command: phenix.autosol Reading effective parameters from autosol.eff The key inano is not in var_type_dict...this means the command-line Wizard needs a conversion in the autosol.py script under 'Translating inputs' or else in excluded_inputs(['write_run_directory_to_file', 'carry_on', 'run', 'copy_run', 'delete_runs', 'display_runs', 'display_facts', 'display_summary', 'display_labels', 'coot', 'dry_run', 'stop', 'params_only', 'sites', 'atom_type', 'sites_file', 'seq_file', 'quick', 'data', 'f_prime', 'f_double_prime', 'labels', 'sites', 'atom_type', 'peak', 'infl', 'high', 'low', 'remote', 'native', 'deriv']) Any ideas? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Parallel Version of Phenix?
by Angelo Rossi 03 Jun '09

03 Jun '09

Hello Phenix Users and Developers: I am new to Phenix and am trying to help a colleague move his project using Phenix from a single workstation to a Linux cluster. My background is chemistry and high performance computing, but I am not intimately knowledgeable about the workings of Phenix. Are there parts of Phenix that can run on a Linux cluster in parallel. I understand that a good part of Phenix is written in python, but there are certainly numerically intensive aspects of structure refinement that could be amenable to parallelization. It would really help if you could provide an overview of those components that are now running in parallel. A search on the net did not reveal information about a parallel version of Phenix. Thank you for your attention and any possible help. Kind regards, A. R. Rossi

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Fixing coordinates in phenix.refine_gui
by AMIT 02 Jun '09

02 Jun '09

Hi All Is it possible to fix only the coordinates(xyz's) of residues or individual atoms in phenix.refine_gui while refining it for rest of the atoms? Any suggestions will be helpful. Thanks in advance Amit. -- AMIT DAS, PROTEIN CRYSTALLOGRAPHY SECTION, SOLID STATE PHYSICS DIVISION, BARC, TROMBAY, MUMBAI-400085. INDIA. Alt E-mail:[email protected] <E-mail%3Aamitdas(a)barc.gov.in> PHONE:+91-22-25594688/4063 FAX:+91-22-25505151

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mutate to polyAla in phenix.automr?
by Francis E Reyes 28 May '09

28 May '09

Is there an option or a phenix.* utility to mutate a MR model to poly ALA before the MR is done? Thanks! FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Failed to carry out AutoBuild_build_cycle: Word too long.
by Gino Cingolani 28 May '09

28 May '09

Hi Folks, does anybody know what this means? My AutoBuild dies off in the middle with this error message ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /home/gino/XTAL/SYN/V1/DASETs/Se3/SAD/REF/AutoBuild_run_2_/TEMP0/RUN_FILE_1' Word too long. ******************************************************************************** Thanks, Gino *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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covalently linked ligand
by Joerg Standfuss 27 May '09

27 May '09

Dear phenix users, I am currently building a model where the ligand is linked via schiff base to a lysine residue. To let phenix know about the link I provide the ligand.cif file and created the link parameter file as described in the manual. The type of link I defined with Jligand as it does not appear in the standard ccp4 library. Unfortunately phenix.refine stops with the error message below when I provide the so created files. It seems phenix has problems to apply the needed ligand modifications ie removing hydrogens and oxygens and stops with the refinement. I have no idea why this doesn't work and am getting a little desperate so any suggestions how to do this properly would be greatly appreciated. Could I use for example elBOW to create the link description? many thanks, Joerg File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/pdb_interpretation.py", line 499, in __init__ mod_mod_id=self.mon_lib_srv.mod_mod_id_dict[apply_data_mod]) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/pdb_interpretation.py", line 771, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/cif_types.py", line 339, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/cif_types.py", line 244, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: H151

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AutoBuild can't align sequence file
by Moritz.Metlitzky＠sbg.ac.at 27 May '09

27 May '09

Hi all, i'm currently trying to solve my structure with phenix and i tried to do it via AutoMR. At first everything works fine, it finds a MR solution, but then i get this error: Chain too short or poor match to sequence: MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL NOTE: chain A (residues 1-304) MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL did not match the input sequence... ignoring alignment and rebuilding segment without sequence information. *************************************** AutoBuild Input failed Sorry, the PDB file and sequence file could not be aligned (with no gaps and >50.0% identity) Please restart the wizard... You have several possibilities to try .... You can set rebuild_in_place=No You can set input_sequence_file=None You can set min_seq_identity_percent to a lower value You can set highest_resno to a higher value You can specify start_chains_list if your PDB file sequence starts with a residue number greater than the number of residues in the sequence. what can i do now? the pdb file has nearly the same sequence (2 mutations) but he says that he can't align them, i use a .dat file for this is this correct? i also have a fasta line in it >... but it doesn't work without this line either. i tried with different phenix versions and have always the same problem Any suggestions would be appreciated.

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refinement of a ligand with alternate conformations in one region but not the other.
by Pascal Egea 26 May '09

26 May '09

Dear All, I am refinining a protein-NAD complex structure at ~1.9A resolution. I have included a main conformation for my NAD ligand but while I see clearly the position for the nicotinamide- first ribose part, my density bifurcates when it comes to the second ribose-adenine. It seems that I have two (at least) conformations for this part of the ligand molecule. Can I refine these two alternate conformations in Phenix knowing that a part of the ligand will be common (have an occupancy of one) while the two other ones will be separate? Do I need to enter two ligand molecules or do I have to do more elaborate things? Last question is it possible that for the variable regions I may end up with a sum of occupancies that is not 1 while for the fixed region it might end up being one? That's three questions for the wizards. Thanks in advance. Pascal Egea UCSF

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Attaching H onto phosphate group and ATP
by Young-Jin Cho 26 May '09

26 May '09

Hello phenix users, I am wondering if phenix.elbow can attach H onto phosphate group for refinement. The reason for that, based on different pH environment, phosphate group should have different charges with respect to how many protons attached. In addition, how can I know normal distance restraints such as ATP? What I only know from the coot is that it shows P-O bond length is 1.61A and P-O bond (delocalized double bond) is 1.5A. The reason for this is, I heard about phosphate ion, if it is protonated, then the bond length of HO-P is longer than that of non-protonated O-P. I want to try if is true for ATP as well. Is there anyone who knows practically testing this fact by using phenix? Thanks in advance, YoungJin

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turbo frodo
by Zhongli Cui 22 May '09

22 May '09

Dear all, I think turbo frodo is a very good software for modelling. I tried to get a licence key from turbo(a)afmb.cnrs-mrs.fr, but got no reply. I would like to know if this software is still in support. Thank you. ---------------- Cui Zhongli Professor, Ph.D Dept. of Microbiology College of Life Sciences Nanjing Agricultural University 1 Weigang, Nanjing, 210095 Jiangsu Province P.R. China. Mail: czl(a)njau.edu.cn Tel: 86-25-84396753 Mob: (0)13951080529

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